CRISPR-Cas Genome Editing and The High School Classroom

By Dan Williams – Suffolk STANYS Biology SAR

A few years ago Bayer Aspirin was advertised as the “Wonder Drug that Works Wonders”, this was Bayer’s attempt to capitalize on the fact that aspirin was a lot more than just a pain medication. 

The more I learn about CRISPR-Cas genome editing systems and I think about their applications in my classroom, I find myself constantly musing: CRISPR-Cas “The Wonder DNA/Enzyme system that works wonders” –I know, the catchphrase needs work.  

It has been a wonder in my classroom, and my hope is that you’ll find in this essay ideas that can spark a renewed sense of wonder in your students. I offer both a set of broad interdisciplinary concepts and practical activities, starting with a view of history and ethical challenges to cutting edge science.

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CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats, sequences in the DNA of bacteria discovered by Yoshizumi Ishino of Osaka University in 1987.  Twenty years later in 2007 scientists including Rodolphe Barrangou of Danisco USA, a yogurt company, demonstrated that the CRISPR sequences along with the action of Cas proteins (CRISPR Associated) act as an adaptive immune system for the bacteria against phages, viruses that kill bacteria.  In 2012 Jennifer Doudna and Emmanuelle Charpentier demonstrated that this bacterial immune system can be fine-tuned for efficiency and ‘programmed’ to target most any gene of choice, opening the door for potential CRISPR-Cas genome editing.  Today, that is what CRISPR is known for, genome editing and its power to change the world.

This little history lesson is actually part of the ‘wonder’ of CRISPR-Cas, consider the diversity in the previous paragraph; a DNA scientist from 1987 examining a gene sequence, a yogurt scientist twenty years later looking to keep vital strains of bacteria safe from phages and a protein scientist five years later manipulating the system in a novel way.  Who would predict that their research could be related?  This leads to a couple of important lessons for our Science students: one is that your research no matter how obscure today is valuable and might change the world.  Two, discoveries do not happen magically like bumping one’s head and seeing the ‘flux capacitor’ but are built on previous work.  Jennifer Doudna states in her book A Crack in Creation that when she was approached by Emmanuelle Charpentier about an interesting bacterial system, she had to do research to learn exactly what Dr. Charpentier was proposing.  Our students today often think, they come up with a great idea and in one school year they are going to do a project that will win the Nobel prize.  Worse, in our Research class culture we encourage this false narrative.  Research is a journey of discovery not a race for a prize.  Examination of the historical experiments that helped us get to where we are today, is an important reminder of that.

Another important part of the history lesson is to remind teachers and students of coding and Bioinformatics.  If Yoshizumi Ishino did not look for unknown, or odd sequences in and around the gene he was studying, who knows when these repeats would have been discovered.  Who knows what unknown or odd sequences lie in wait in genomes waiting to be discovered now?  This is actually a pretty simple coding exercise; download a genome FASTA file and write a code to search for the longest repeated string, or the string repeated most often, etc.  Are we teaching coding in our classrooms, or in our science labs? The history or CRISPR-Cas suggests that we should.  Maybe our students can discover something big?

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Likewise, how much are we teaching Bioinformatics?  Barrangou’s discovery that CRISPR-Cas has adaptive immunity is an exercise in Bioinformatics; the spacer regions of the CRISPR locus are viral DNA sequences, easy enough to discover with BLAST searches.  Today scientists around the world are finding new applications for CRISPR-Cas, and discovering new varieties of the system by simply examining BLAST hits and doing phylogenetic analysis.  Often our students think of phylogeny as just an exam question, but it is leading to new discoveries every day.  Coding and Bioinformatics are open ended discovery research, a journey into the unknown –not a eureka moment.  Work like this is changing the world.  Our students can be doing this work –and its free, you just need a computer! Some suggested activities are listed at the end of this article.  

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The history lesson is nice, but most people think of CRISPR and they want genome editing, cures for cancer or real living unicorns.  That is the next area of wonder.  The CRISPR-Cas system is programmable genetic engineering and surprisingly easy to model and do in the high school classroom.  It is truly the ‘wonder enzyme system’ that is both simple and complex at the same time.  Students can research diseases they wish to cure, or traits they want to change and design, and test a CRISPR-Cas system to investigate if it is possible.  It sounds too simple and too good to be true, but you might be surprised at what can actually be done.  

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Using online tools completely, students can find a gene of interest (https://www.ncbi.nlm.nih.gov/), discover if it has a CRISPR-Cas locus (https://chopchop.cbu.uib.no/ ), verify off-target hits and simulate if their target was correct with in silico PCR (https://genome.ucsc.edu/).  They can test any hypothesis they want to see if a CRISPR experiment is possible.  Even better, if your school has the resources it can order a CRISPR-Cas system from companies like https://www.addgene.org/ and test it in a wet lab situation.  Last year at Cold Spring Harbor’s scientific meeting “Genome Engineering: CRISPR Frontiers”, I learned that scientists are testing the viability of their CRISPR designs by simply ordering the system from a company like Addgene and cutting a plasmid that contains the target sequence; if the plasmid is cut, then the designed CRISPR-Cas works.  It is easy enough to cut a plasmid in a classroom and run it on a gel electrophoresis as we have been doing that for years.  Therefore, whether you want your students to design a virtual experiment or test a real one, CRISPR-Cas can be done in the high school laboratory.  

Oh and did I forget to mention the ethical discussions that can and should arise?  In designing a CRISPR-Cas experimental system like above, students should start to realize how it is not fool proof, things can go wrong.  What unforeseen things could be lurking?  It is one thing to be cutting a plasmid, but what if you are cutting a patient’s DNA?  We know so little about our own genomes; what risks would be acceptable?  What is too much?  Risk is one thing for a patient who is sick and or dying, but what about gene enhancements?  

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The ethics of CRISPR-Cas make our GMO discussions look quaint.  The promise of CRISPR-Cas is that it can make genome editing much faster, cheaper and easier than ever before.  In our classrooms we should be having the discussions of the differences between therapeutic gene editing, preventative gene editing and gene insertion.  Therapeutic gene editing is where one fixes a disease with a known wild type variant like sickle cell being fixed with normal hemoglobin.  Preventative gene editing, proactively altering a person’s genes who has a ticking time bomb in their DNA (e.g. BRACA –breast cancer).  Finally, gene insertion where novel traits are given to an organism, making a pest-resistant tomato for instance or as some would fantasize –unicorns and other mythical creatures.  Of course there are many pros and cons to discuss in each instance.  Like the discussion of GMO’s there are no easy answers, however these questions are going to be weighed by our society in the very near future.  Our students must learn how to examine each issue with critical thinking, using evidence based justifications to form their opinions.   

By now if you are still reading this you might be feeling overwhelmed, thinking to yourself that you could never do all of this.  First of all, as teachers we know we can never do everything –but what makes CRISPR-Cas so wonderful is that it provides so many SOME-things that CAN be done.  It is truly the wonder enzyme system that does wonders, and has so many applications in the classroom from which you can pick and choose.  Students can model, design experiments, justify claims with evidence all from CRISPR-Cas.

Finally, most importantly, you do not have to invent the wheel, there are many tutorials and educational material out there.  If you are looking for a great place to start, the Innovative Genomics Institute (https://innovativegenomics.org/), founded by Dr. Doudna herself, has incredible resources ready for use in the classroom and they will respond to your inquiries with answers.

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In addition, I have written several activities that I am currently trying with my students and would be happy to share editable copies with anyone who asks –to try it in your own classroom, just send me an email at dan.williams@shlterisland.k12.ny.us

Evolution 3D Printing Hominids Fossils Phenomena

By Dan Williams  

Many of us are familiar with the famous quote from Theodosius Dobzhansky, that “nothing in Biology makes sense except in the light of evolution.”  I am not alone when I state that evolution is one of my favorite topics within Biology. Whether its examining derived traits within butterflies, predator prey relationships, or how a complex molecule like the ATP synthase evolved, the topics in evolution are varied, complex, and fascinating.  

Evolution however, is often the most misunderstood topic in Biology and despite our best intentions, we perpetuate the misconceptions with our classroom examples, exercises, and labs.  Please do not misunderstand me, I am not suggesting at all that I am any different –regardless of my best efforts, I too, unknowingly, have passed on misconceptions about evolution to my students.  Luckily, there are new tools to teach evolution which will inspire students with wonder, have them question phenomena, and help uncover and address the misconceptions we have built into our teaching of evolution.   

One such tool is the three dimensional printing of fossil scans.  It is easy to use, inexpensive, powerful and works well within a New York State Science Learning Standards (NYSSLS) environment.  Fossil scans are accurate 3D renderings made by paleontologists of real fossils within the field which can be freely downloaded from public databases for printing on common 3D printers.  At the conclusion of this article I have provided links to resources that can be used to download and 3D print fossils for your classroom.

3D Printed Fossil Crania (L-R H. Heidelbergensis, H. naledi, H. Neanderthalensis, H. Sapiens)

A few months back, I was beyond excited when I cleaned off my new fossil crania scan from the 3D printer.  It was of a new hominid that was in the news called Homo naledi.  My students were also excited, they asked lots of questions about naledi, its discovery and human evolution in general.  I decided to perform an impromptu experiment with my new fossil crania and some other 3D prints I had laying around. I placed before my students the unidentified crania of Homo sapiens, Homo neanderthalensis, Homo heidelbergensis, Homo erectus and the new naledi print.  I asked my students to place them in “evolutionary age order” –in other words, from the more primitive to the most advanced species.

Not surprisingly, my students placed the crania in order: small too large.  Intuitively, this made sense to them, however it was completely wrong. Homonaledi, the smallest crania, actually only dates to around 300,000 years ago –concurrent with Neanderthals and late Heidelbergensis –hardly the most ancient.  Evolution, we know is change, not progressive change, just change. My students “knew this.” We always talked about how extinction is evolution (bad change for the extinct), I even had slides showing that Neanderthal brains were larger than ours (implying they might have been more intelligent than us) but they died out and here we are.  I emphasize lots of examples of non-progressive change in my lessons. None of this mattered when my students were faced with objects they could touch, look at and observe. Obviously my “talking about evolution,” and “showing examples of evolution” was not enough to dispel the myth that evolution is progress.

Through self-reflection I realized that I had reinforced this misconception.  Whether it’s peppered moths in industrial England, the fastest cheetah catching the slowest gazelle, Hardy Weinberg with M&M’s or the beaks of finches, all of my hands on activities double down on the idea that evolution is progressive change.   

Here on the desk in front of me, however, was a phenomenon; hominid crania did not progressively get larger –what on earth was going on?

If student interest and excitement on a topic is measured in the quantity, quality, and decibel level of questions, this phenomenon was a home run!  I had to settle my students down, restore order, and respond to each question they had with questions of my own –they claimed their brains hurt after only a few enjoyable minutes.

This would be a great story if it ended there, but the 3D fossil scans provided so much more than a quick phenomenon to start teaching a unit.  We examined the fossils scans, visually observing the presence or absence of features and measuring differences between the crania with calipers.  Claims were made based on the observations, data charts, and graphs were created to examine the evidence of the crania. The reasoning of the students’ hypotheses were hotly contended between groups.

Students measuring 3D printed crania

I have now 3D printed fossil scans of mandibles, as well from all of the aforementioned species, plus Australopithecus afarensis and Australopithecus boisei.  These provide additional data to examine so that my students can make claims about diet and the processing of food. In some ways, the mandibles are easier than crania, as tooth diameter (buccolingual width) is a more consistent measurement for students to obtain and compare. 

Students made distant matrices of their data from the crania and the mandibles (separately).  They then sketched cladograms based on their claims of ancestral and derived traits. They have used an erectus 3D print to determine ancestral traits in crania and the boisei 3D print for ancestral traits in mandibles.  

While the discussions were valuable, the students found the cladograms difficult to generate by hand.  Most cladogram builders available today are for DNA comparisons, however I found an easy to use app developed David Dobson of Guilford College called “Simple Clade.”  It was invaluable in creating cladograms, manipulating for maximum parsimony for unbiased data analysis of the student claims. The cladograms however, did not stop the arguments that had now generated among the students.  The 3D prints provided phenomena that was not easy to explain, and fostered many claims on evolution that students actually wanted to explore. Best of all, none of the claims were based on evolution as progress.

Like most biology teachers, evolution is a major passion of mine, hominid evolution specifically.  I also find that hominids interest students as much (or almost as much) as dinosaurs. Using hominids as examples captivates students and provides ample phenomena to study.  I have read about human evolution for years, watched videos about it, examined anatomical diagrams, but until I held 3D prints of hominid skulls in my hands, I can honestly say I did not fully understand human evolution.  

The same can be said for my students, as well.  We discussed evolution, and I gave traditional examples of evolution, but until they held the 3D scans of fossils in their hands, they had misconceptions.  I never knew my traditional methods of teaching evolution led to misconceptions, working with 3D printed fossil scans not only helped uncover the students misconceptions, but also helped clear them up.

If you have any questions or are looking for the specific methods of how to download and 3D print your own fossil collection, please e-mail me at dan.williams@shelterisland.k12.ny.us

Useful Links

Fossil Databases:

African Fossils https://africanfossils.org/search

Morphosource https://www.morphosource.org/

Educational Links

iDigfossils http://www.idigfossils.org/

Human Evolution Teaching Materials Project https://www.hetmp.com/

Paleoanthropology

John Hawks YouTube Channel https://www.youtube.com/channel/UCVfaXPlLTPTjbU-ed9VMBfg

Programs Used

SimpleClade http://guilfordgeo.com/simpleclade/index.html

MeshLab http://www.meshlab.net/

MeshMixer http://www.meshmixer.com/

MakerBot https://www.makerbot.com/

We Win Success by Failing.

I’m bored with talking about success. By any metric, I’ve had the good fortune to enjoy a lot of success in my career as an educator. But I also fail a lot. And I know that I’m not alone. Failure is a significant part of educating kids. I don’t mean kids failing (hopefully that’s pretty diminished), I mean teachers failing to do the things they try to do. Things not working as planned. Mistakes being made. This kind of failure is more than just a thing that happens sometimes, it’s a significant part of the job. And it’s totally normal and expected.

So why do we hide it?

If you look at any public collection of educators, you’ll quickly see that discussion of success is much more common than conversations about failure. Any look at the #eduTwitter-scape or any of the Facebook groups for teachers is basically a wall-to-wall display of success. Kids doing amazing work. Teachers trying new things, and being delighted with the results. Everything working out exactly as planned (or even better than that). Which is lovely, but as far as I’m concerned, it’s not particularly reflective of the reality of teaching. Teaching is hard creative work, and like all hard creative work, people fail a lot.

The issue is even more glaring in science education, where teachers teach a field of endeavor that proceeds by failing. The central role of falsification in the scientific process is so essential that only presenting success not only warps perceptions of reality; it can distort our very understanding of it. And yet, we still pretend like things succeed in our classes more than they fail.

It’s easy to understand why this is the case. Generally speaking, people want to be perceived at their best, and for most people, their “best” is not when things they are trying to do aren’t working. It takes a degree of confidence to be willing to show one’s posterior on a regular basis. But in my experience, giving failure a public perch leads to a level of improvement in practice and product that is just not possible if all you talk about is success. Learning is nothing if not all about correction.

Assuming you agree with the above, the question becomes how to build a place for failure in your public life. I won’t pretend to have all of the answers, but I do have a few ideas that have worked well for me:

  1. Keep everything in Beta. Beta testing refers to the practice in technology development wherein a working, imperfect, version of a product is turned over to a large group of people to use. This everyday usage then provides the developers with a list of imperfections that would otherwise remain undiscovered if the developers were the only ones doing the product-testing. This philosophy is easily applied to education. The work that teachers do and the materials they create should live in a state of constant beta testing. By taking the default stance that work is imperfect, there is less discomfort when the imperfections in that work are discovered. Of course, this type of thinking is only helped by a willingness to make your work available to a vast professional learning network under pretty open terms of usage. Fortunately, in the modern era of easy-to-build webspace and free to distribute licensing, it’s trivial to set up a system wherein you can be a perennial beta tester. All it requires is a willingness to do it.

  2. Keep a Resume of Failures. I first discovered the concept of the resume of failures when I read this article. The example resumes that it included lead me to put up my own. I think more people should do this, and I hope that doing so on my end leads some of the tens of thousands of people who interact with myself and my digital footprint every year to realize that failing is a large part of why I’ve had the career that I’ve had. Who I am as an educator, and what I do is arguably much more a result of the failures that I’ve had in my career than it is of my successes1.

  3. Reflect on failures (and successes). I am a huge fan of reflective practice. My reflection tends to happen in public spaces. I find a lot of value in thinking aloud if for no other reason than that it invites correctives from a maximal number of wise minds. But even if a public airing of your reflective practice isn’t something that appeals to you, the act of reflecting itself is invaluable for learning from your experiences. There are a variety of tools that you can use to help you reflect, ranging from a notebook, a simple .txt file, or something a little more formal like 750Words or a blog. However you do it, the trick is to make sure that you actually stick to a routine of regularly engaging in reflection on the work that you are doing with the understanding that the purpose of that reflection is not to whinge about imperfection, but instead to think about how to improve.

These are three relatively easy ways to build a space for considering failure into your professional life. As always, it might be too much to try to do all three of the above at the same time. But the point isn’t to do everything that’s suggested (or even anything that’s suggested). Instead, it’s to work to make a space in your working life for acknowledging that however good we are as educators, however fortunate we have been in our work, we still fail a lot.

Cool Tools: Loopy

Systems thinking is as important as it is hard.  As we look at the New York State Science Learning Standards, we see a clear role for systems thinking.  Systems and System Processes is one of the Cross-Cutting Concepts, and Developing and Using Models is a Science Practice.  It should be obvious to all of us that where we are going as a state is very much to system-land.

There are many ways that we can model system dynamics.  Many of us model systems in our classrooms whenever we engage in “simulations”, or other types of modeling activities.  And I’m sure most readers are well aware of the various interactive computational simulations that have been created for students to work with.  But there are not a whole lot of computational resources that allow students to construct relatively robust models of systems for their own investigation.  This is mostly because programming computers is relatively difficult. As such it’s not often tenable to train students in how to create a computational tool prior to having them use it.

Which is where Loopy comes in.  Loopy is a very simple systems dynamics modeling tool where anyone can create a system and then see how its dynamics affect the system.  No programming is required, and the tutorial should take anyone <5 minutes to be able to render a system of their own interest.

Here’s an example of Loopy at work in a simple food web model that I created for this article:

See?  Not that hard (also, I totally understand that it’s “not that good”).

Tools like Loopy can help give students opportunities to model systems, without the high cost of entry that usually accompanies computational model construction.